In "This Is Not Happening," Scully sees a ghostly vision of Mulder where he is speaking but cannot be heard. This always seemed to me to be a call back to a similar vision Scully has of her father in "Beyond the Sea." Was this intentional?
Good catch, Adam, and yes, it was indeed. We loved whenever we were able to find these kinds of connections between episodes, and it's surprising how many times it happened over the course of the series. They were like invisible threads that we would pick up and knit together, not having realized they were there until then.